Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates

Abstract

Sequencing the large genomes of sharks. We focused on the brownbanded bamboo shark Chiloscyllium punctatum, for which we recently tabled embryonic stages 8 , and the cloudy catshark Scyliorhinus torazame. Their whole genomes, measured to be approximately 4.7 and 6.7 Gbp, respectively, were sequenced de novo to obtain assemblies including megabase-long scaffolds (Supplementary Note 1.1). We also assembled the genome of the whale shark Rhincodon typus using short sequence reads previously generated 3 (Supplementary Note 1.2). Using these genome assemblies, we performed genome-wide gene prediction, assisted by transcript evidence and protein-level homology to other vertebrates. The obtained genome assemblies and gene models exhibit high coverage (Supplementary Fig. 1), and of these, the bamboo shark genome assembly achieved the highest continuity (N50 scaffold length, 1.9 Mbp) and completeness (97% of reference orthologues identified at least partially). Using the novel gene models, we constructed orthologue groups encompassing a diverse array of vertebrate species (see below). Our products outperform existing

Electroreception in marine fishes: chondrichthyans

“…Undoubtedly, this line of research would benefit from sequencing the genomes of key elasmobranch species and detailed studies on the molecular mechanisms that underlie chondrichthyan electroreception. Currently, the genomic sequences are known for a handful of the nearly 1300 chondrichthyans including: the whale shark Rhincodon typus (Smith 1828) (Read et al, ), C. punctatum , cloudy catshark Scyliorhinus torazame (Tanaka 1908) (Hara et al, ) , white shark Carcharodon carcharias (Linnaeus 1758) (Marra et al, ) and elephant shark Callorhinchus milii (Bory de Saint‐Vincent 1823) (Venkatesh et al, ). Leucoraja erinacea is the nearest model elasmobranch species to date and the assembly of its genome is underway at http://www.skatebase.org (Wang et al, ).…”

“…Leucoraja erinacea is the nearest model elasmobranch species to date and the assembly of its genome is underway at http://www.skatebase.org (Wang et al, ). These genetic studies have shown that some benthic associated species have very few odorant receptor genes expressed in the olfactory epithelium (Hara et al, ; Venkatesh et al, ) and it is likely that further genomic screens could lead to insights about chondrichthyan electrosensory phenotypes.…”

Involvement of HGF/MET signaling in appendicular muscle development in cartilaginous fish

“…In our study, Hgf expression was detected throughout the pectoral fin buds, with intensified expression in the anterior and posterior parts. In fact, the orthologies of the Hgf and c‐Met genes analyzed for S. torazame (Adachi et al., ) and S. canicula (in this study) are suggested by their high cross‐species similarity (Supporting Information Figure ) and the small numbers of synonymous substitutions per site (0.081 and 0.019, respectively, compared with the inter‐order count of over 0.400) (Hara et al., ).…”

“…A recent study reported that in a different species in the genus Figure S1) and the small numbers of synonymous substitutions per site (0.081 and 0.019, respectively, compared with the inter-order count of over 0.400) (Hara et al, 2018).…”

Evolution of nodal and nodal‐related genes and the putative composition of the heterodimers that trigger the nodal pathway in vertebrates

“…The differential retention of genes could be seen as a stochastic process, in which the resulting differences in gene complement do not translate into functional consequences. This could be due to some functional redundancy among the paralogs that could work as a backup (i.e., functionally overlapping paralogues) in the case one is lost or inactivated (Albalat & Cañestro, 2016;Cañestro, Catchen, Rodriguez-Mari, Yokoi, & Postlethwait, 2009;Félix & Barkoulas, 2015), or a byproduct of divergent nature of the genomic location in which the duplicates are found (Hara, Takeuchi, et al, 2018;Hara, Yamaguchi, et al, 2018). Alternatively, it is also possible that the presence of multiples copies opens opportunities for the emergence of biological novelties (Force et al, 1999;Hughes, Hughes, Howell, & Nei, 1994;Ohno, 1970;Ohno, Wolf, & Atkin, 1968;Zhang, 2003).…”